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- PDB-5e1h: Ricin toxin in complex with neutralizing single chain monoclonal ... -

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Basic information

Entry
Database: PDB / ID: 5e1h
TitleRicin toxin in complex with neutralizing single chain monoclonal antibodies (VHHs)
Components
  • F8(JOB10) VHH antibody
  • Ricin
KeywordsTOXIN/IMMUNE SYSTEM / Ricin toxin / VHHs / TOXIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / AMP binding / defense response / toxin activity / carbohydrate binding / killing of cells of another organism / negative regulation of translation
Similarity search - Function
Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 ...Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Few Secondary Structures / Irregular / Immunoglobulins / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesRicinus communis (castor bean)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.032 Å
AuthorsRudolph, M.J. / Vance, D. / Shoemaker, C. / Mantis, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201400021C United States
Citation
Journal: Proteins / Year: 2016
Title: Structural analysis of nested neutralizing and non-neutralizing B cell epitopes on ricin toxin's enzymatic subunit.
Authors: Rudolph, M.J. / Vance, D.J. / Cassidy, M.S. / Rong, Y. / Shoemaker, C.B. / Mantis, N.J.
#1: Journal: To Be Published
Title: Crystal structures of ricin toxin's enzymatic subunit (RTA) in complex with neutralizing and non-neutralizing single-chain antibodies
Authors: Rudolph, M.J. / Mantis, N.
History
DepositionSep 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references / Source and taxonomy / Structure summary
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ricin
B: F8(JOB10) VHH antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6635
Polymers42,5572
Non-polymers1063
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-37 kcal/mol
Surface area16670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.472, 91.775, 95.143
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-483-

HOH

21A-485-

HOH

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Components

#1: Protein Ricin /


Mass: 28903.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Production host: Escherichia coli (E. coli) / References: UniProt: P02879, rRNA N-glycosylase
#2: Antibody F8(JOB10) VHH antibody


Mass: 13653.028 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 100 mM BisTris pH 5.5, 25% PEG 3000, 260 mM NaCl, and 10 mM Tris (2carboxyethyl)phosphine hydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twinOperator: -k,-h,-l / Fraction: 0.04
ReflectionResolution: 2.03→50 Å / Num. obs: 24972 / % possible obs: 98.7 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.092 / Rrim(I) all: 0.152 / Χ2: 0.89 / Net I/av σ(I): 11.396 / Net I/σ(I): 4 / Num. measured all: 148336
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Num. unique allCC1/2Χ2% possible allRpim(I) allRmerge(I) obsRrim(I) all
2.03-2.075.112240.2260.50796.8
2.07-2.15.311940.290.51797.50.933
2.1-2.145.412350.5530.472990.714
2.14-2.195.512360.3840.50398.70.649
2.19-2.235.412270.3980.52598.80.671
2.23-2.295.512170.3080.66296.80.559
2.29-2.346.212380.840.54799.10.452
2.34-2.416.312390.8460.53799.10.4240.978
2.41-2.486.212400.8750.57199.30.3350.7650.836
2.48-2.566.212530.9080.60999.10.2570.5850.641
2.56-2.656.112480.9310.621990.2080.4710.516
2.65-2.765.712200.940.68497.80.1630.3590.395
2.76-2.886.312610.9760.67499.10.120.2810.306
2.88-3.036.412490.9810.74499.70.0950.2230.243
3.03-3.226.412500.9870.8699.40.0740.170.185
3.22-3.476.212710.9871.21399.70.0620.1390.153
3.47-3.826.112590.9921.50198.40.0490.1130.123
3.82-4.376.612720.9931.78999.60.0390.0930.101
4.37-5.51612810.9931.79298.10.0360.0820.09
5.51-50613580.9921.93998.70.0380.0840.093

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.03 Å45.89 Å
Translation2.03 Å45.89 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.032→45.888 Å / FOM work R set: 0.7661 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.56 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2567 1272 5.1 %
Rwork0.2041 23685 -
obs0.2052 24964 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.538 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso max: 109.17 Å2 / Biso mean: 43.21 Å2 / Biso min: 14.89 Å2
Baniso -1Baniso -2Baniso -3
1-9.7195 Å20 Å2-0 Å2
2--3.7698 Å2-0 Å2
3----13.4893 Å2
Refinement stepCycle: final / Resolution: 2.032→45.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2971 0 3 122 3096
Biso mean--64.17 42.43 -
Num. residues----382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063047
X-RAY DIFFRACTIONf_angle_d1.0484143
X-RAY DIFFRACTIONf_chiral_restr0.073462
X-RAY DIFFRACTIONf_plane_restr0.004541
X-RAY DIFFRACTIONf_dihedral_angle_d13.4871087
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0334-2.11470.34221570.3052533269092
2.1147-2.21090.31861500.27882593274393
2.2109-2.32730.29141320.27362562269493
2.3273-2.47290.32211010.25322660276196
2.4729-2.66350.29151490.24432626277594
2.6635-2.93090.29881390.22692616275594
2.9309-3.35360.26231520.20422639279194
3.3536-4.21960.2241290.16272681281095
4.2196-21.11850.19511210.15752775289694
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.34360.04661.42273.15180.48944.76590.05670.3974-0.1792-0.53-0.1026-0.24360.49161.12190.11740.39220.18810.06920.3520.06910.299225.235835.741369.4247
23.2571-0.2519-1.08626.2737-2.33557.09940.2338-0.1111-0.301-0.2332-0.253-0.0741.00180.04960.01150.28840.04530.02540.19020.04580.213318.414730.433683.2551
31.21280.31190.98051.6949-1.45246.8715-0.1653-0.08830.19450.12130.13190.1861-0.7726-0.59480.03140.27440.12740.00750.20490.010.246713.599545.859472.3286
45.30771.4158-0.94752.66230.50344.4194-0.20970.36130.1363-1.2435-0.4885-0.7192-0.0742-0.12610.65770.551-0.1273-0.03430.6480.13760.3406-7.851515.145106.1133
52.02130.998-1.00332.0042-5.02638.9601-0.0057-0.00920.2628-0.50290.50560.844-0.2035-0.2821-0.52510.309-0.0891-0.07360.47270.09510.4908-7.475118.20499.5701
69.27772.4771-1.53348.5299-3.74258.27570.0373-0.180.557-0.16950.05070.3811-0.5012-0.2294-0.12380.213-0.07110.0570.4070.02220.35870.56423.466396.9335
71.8467-0.64134.48050.2286-1.55741.99990.1532-0.40760.17470.365-0.1957-0.2706-0.47830.1130.09880.304-0.09190.02230.54360.10520.35396.08718.492105.6528
86.3831.17840.64227.6674-1.11542.0115-0.2861-0.0551-1.0729-0.867-0.1272-0.67360.71591.49950.42010.44990.13520.13870.49350.10030.46796.05713.222394.6696
95.0878-0.4685-0.45948.8332-4.83349.7679-0.08560.2114-0.5609-1.03280.59140.60380.8978-0.9362-0.46460.5008-0.205-0.01320.48360.07980.3512-3.69616.081692.8124
103.29341.1626-2.97429.8786-3.47616.1229-0.20850.0563-0.4095-0.52540.43410.79820.7815-0.7881-0.28990.3699-0.2252-0.02550.49910.13470.4356-4.99815.423297.2903
113.072.9046-3.30216.1833-2.88057.57570.2842-0.8743-0.57610.4402-0.7692-0.59290.23930.77290.40650.3282-0.14-0.01170.60850.16030.40680.641613.7418107.6655
126.50010.1007-0.75836.3482-1.16915.16610.1878-0.6781-0.05510.2875-0.2339-0.1325-0.40830.2160.03230.3952-0.11660.03710.41950.09530.28727.107726.093997.7958
137.2906-1.00351.01153.0386-0.32314.0220.195-0.9493-0.73580.6374-0.31190.0480.30910.0670.03060.1425-0.3226-0.03760.83820.20170.4689-4.473911.2282113.9298
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:56)A5 - 56
2X-RAY DIFFRACTION2chain 'A' and (resseq 57:122)A57 - 122
3X-RAY DIFFRACTION3chain 'A' and (resseq 123:262)A123 - 262
4X-RAY DIFFRACTION4chain 'B' and (resseq 2:17)B2 - 17
5X-RAY DIFFRACTION5chain 'B' and (resseq 18:25)B18 - 25
6X-RAY DIFFRACTION6chain 'B' and (resseq 26:39)B26 - 39
7X-RAY DIFFRACTION7chain 'B' and (resseq 40:51)B40 - 51
8X-RAY DIFFRACTION8chain 'B' and (resseq 52:67)B52 - 67
9X-RAY DIFFRACTION9chain 'B' and (resseq 68:76)B68 - 76
10X-RAY DIFFRACTION10chain 'B' and (resseq 77:83)B77 - 83
11X-RAY DIFFRACTION11chain 'B' and (resseq 84:99)B84 - 99
12X-RAY DIFFRACTION12chain 'B' and (resseq 100:122)B100 - 122
13X-RAY DIFFRACTION13chain 'B' and (resseq 123:129)B123 - 129

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